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  1. Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5–245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites...

    Authors: Girish Beedessee, Kanako Hisata, Michael C. Roy, Noriyuki Satoh and Eiichi Shoguchi
    Citation: BMC Genomics 2015 16:941
    Content type: Research article Published on:

  2. Bemisia tabaci is one of the most damaging agricultural pests world-wide. Although its control is based on insecticides, B. tabaci has developed resistance against almost all classes o...

    Authors: Aris Ilias, Jacques Lagnel, Despoina E. Kapantaidaki, Emmanouil Roditakis, Costas S. Tsigenopoulos, John Vontas and Anastasia Tsagkarakou
    Citation: BMC Genomics 2015 16:939
    Content type: Research article Published on:

  3. Penicillium chrysogenum is a filamentous fungus that is employed as an industrial producer of β–lactams. The high β–lactam titers of current strains is the result of a classical strain...

    Authors: Oleksandr V. Salo, Marco Ries, Marnix H. Medema, Peter P. Lankhorst, Rob J. Vreeken, Roel A. L. Bovenberg and Arnold J. M. Driessen
    Citation: BMC Genomics 2015 16:937
    Content type: Research article Published on:

  4. Several statistical tools have been developed to identify genes mutated at rates significantly higher than background, indicative of positive selection, involving large sample cohort studies. However, studies ...

    Authors: Pratik Chandrani, Pawan Upadhyay, Prajish Iyer, Mayur Tanna, Madhur Shetty, Gorantala Venkata Raghuram, Ninad Oak, Ankita Singh, Rohan Chaubal, Manoj Ramteke, Sudeep Gupta and Amit Dutt
    Citation: BMC Genomics 2015 16:936
    Content type: Research article Published on:

  5. Salvia diterpenes have been found to have health promoting properties. Among them, carnosic acid and carnosol, tanshinones and sclareol are well known for their cardiovascular, antitum...

    Authors: Fotini A. Trikka, Alexandros Nikolaidis, Codruta Ignea, Aphrodite Tsaballa, Leto-Aikaterini Tziveleka, Efstathia Ioannou, Vassilios Roussis, Eleni A. Stea, Dragana Božić, Anagnostis Argiriou, Angelos K. Kanellis, Sotirios C. Kampranis and Antonios M. Makris
    Citation: BMC Genomics 2015 16:935
    Content type: Research article Published on:

  6. In the past decade the Göttingen minipig has gained increasing recognition as animal model in pharmaceutical and safety research because it recapitulates many aspects of human physiology and metabolism. Genome...

    Authors: Tobias Heckel, Roland Schmucki, Marco Berrera, Stephan Ringshandl, Laura Badi, Guido Steiner, Morgane Ravon, Erich Küng, Bernd Kuhn, Nicole A. Kratochwil, Georg Schmitt, Anna Kiialainen, Corinne Nowaczyk, Hamina Daff, Azinwi Phina Khan, Isaac Lekolool…
    Citation: BMC Genomics 2015 16:932
    Content type: Research article Published on:

  7. Transcriptomics reveals the existence of transcripts of different coding potential and strand orientation. Alternative splicing (AS) can yield proteins with altered number and types of functional domains, sugg...

    Authors: Delasa Aghamirzaie, Dhruv Batra, Lenwood S. Heath, Andrew Schneider, Ruth Grene and Eva Collakova
    Citation: BMC Genomics 2015 16:928
    Content type: Research article Published on:

  8. Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample materi...

    Authors: Florian Mertes, Björn Lichtner, Heiner Kuhl, Mirjam Blattner, Jörg Otte, Wasco Wruck, Bernd Timmermann, Hans Lehrach and James Adjaye
    Citation: BMC Genomics 2015 16:925
    Content type: Research article Published on:

  9. The increased multi-omics information on carefully phenotyped patients in studies of complex diseases requires novel methods for data integration. Unlike continuous intensity measurements from most omics data ...

    Authors: SungHwan Kim, Jose D. Herazo-Maya, Dongwan D. Kang, Brenda M. Juan-Guardela, John Tedrow, Fernando J. Martinez, Frank C. Sciurba, George C. Tseng and Naftali Kaminski
    Citation: BMC Genomics 2015 16:924
    Content type: Methodology article Published on:

  10. Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved...

    Authors: David Greenald, Justin Jeyakani, Bernd Pelster, Ian Sealy, Sinnakaruppan Mathavan and Fredericus J. van Eeden
    Citation: BMC Genomics 2015 16:923
    Content type: Research article Published on:

  11. Within the genetic methods for estimating effective population size (N e ), the method based on linkage disequilibrium (LD) has advantages over ot...

    Authors: María Saura, Albert Tenesa, John A. Woolliams, Almudena Fernández and Beatriz Villanueva
    Citation: BMC Genomics 2015 16:922
    Content type: Research article Published on:

  12. Genomic selection (GS) has become a commonly used technology in animal breeding. In crops, it is expected to significantly improve the genetic gains per unit of time. So far, its implementation in plant breedi...

    Authors: Dario Fè, Fabio Cericola, Stephen Byrne, Ingo Lenk, Bilal Hassan Ashraf, Morten Greve Pedersen, Niels Roulund, Torben Asp, Luc Janss, Christian Sig Jensen and Just Jensen
    Citation: BMC Genomics 2015 16:921
    Content type: Research article Published on:

  13. Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although...

    Authors: Ashley N. Luck, Kathryn G. Anderson, Colleen M. McClung, Nathan C. VerBerkmoes, Jeremy M. Foster, Michelle L. Michalski and Barton E. Slatko
    Citation: BMC Genomics 2015 16:920
    Content type: Research article Published on:

  14. The σ54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a ...

    Authors: Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay and Pavel S. Novichkov
    Citation: BMC Genomics 2015 16:919
    Content type: Research article Published on:

  15. Pathway enrichment analysis is a useful tool to study biology and biomedicine, due to its functional screening on well-defined biological procedures rather than separate molecules. The measurement of malfuncti...

    Authors: Xiangtian Yu, Tao Zeng and Guojun Li
    Citation: BMC Genomics 2015 16:918
    Content type: Methodology article Published on:

  16. The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resis...

    Authors: Joelle Amselem, Marielle Vigouroux, Simone Oberhaensli, James K. M. Brown, Laurence V. Bindschedler, Pari Skamnioti, Thomas Wicker, Pietro D. Spanu, Hadi Quesneville and Soledad Sacristán
    Citation: BMC Genomics 2015 16:917
    Content type: Research article Published on:

  17. Gray Leaf Spot (GLS causal agents Cercospora zeae-maydis and Cercospora zeina) is one of the most important foliar diseases of maize in all areas where the crop is being cultivated. Although in the USA the situat...

    Authors: Jafar Mammadov, Xiaochun Sun, Yanxin Gao, Cherie Ochsenfeld, Erica Bakker, Ruihua Ren, Jonathan Flora, Xiujuan Wang, Siva Kumpatla, David Meyer and Steve Thompson
    Citation: BMC Genomics 2015 16:916
    Content type: Research article Published on:

  19. Effective management and treatment of cancer continues to be complicated by the rapid evolution and resulting heterogeneity of tumors. Phylogenetic study of cell populations in single tumors provides a way to ...

    Authors: Ayshwarya Subramanian and Russell Schwartz
    Citation: BMC Genomics 2015 16(Suppl 11):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

    The Erratum to this article has been published in BMC Genomics 2016 17:348

  20. It is well understood that distinct communities of bacteria are present at different sites of the body, and that changes in the structure of these communities have strong implications for human health. Yet, ch...

    Authors: Mitch Fernandez, Juan D Riveros, Michael Campos, Kalai Mathee and Giri Narasimhan
    Citation: BMC Genomics 2015 16(Suppl 11):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

  21. The advance of high-throughput sequencing has made it possible to obtain new transcriptomes and study splicing mechanisms in non-model organisms. In these studies, there is often a need to investigate the tran...

    Authors: Shuhua Fu, Aaron M Tarone and Sing-Hoi Sze
    Citation: BMC Genomics 2015 16(Suppl 11):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

  22. Traditional approaches to studying molecular networks are based on linking genes or proteins. Higher-level networks linking gene sets or pathways have been proposed recently. Several types of gene set networks...

    Authors: Chayaporn Suphavilai, Liugen Zhu and Jake Y Chen
    Citation: BMC Genomics 2015 16(Suppl 11):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

  23. Many supervised learning algorithms have been applied in deriving gene signatures for patient stratification from gene expression data. However, transferring the multi-gene signatures from one analytical platf...

    Authors: Segun Jung, Yingtao Bi and Ramana V Davuluri
    Citation: BMC Genomics 2015 16(Suppl 11):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

  24. DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technolog...

    Authors: Jacob Porter, Ming-an Sun, Hehuang Xie and Liqing Zhang
    Citation: BMC Genomics 2015 16(Suppl 11):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

  25. Peptide sequence assignment is the central task in protein identification with MS/MS-based strategies. Although a number of post-database search algorithms for filtering target peptide spectrum matches (PSMs) ...

    Authors: Xijun Liang, Zhonghang Xia, Ling Jian, Xinnan Niu and Andrew Link
    Citation: BMC Genomics 2015 16(Suppl 11):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 11

  26. Male sterility is an important mechanism for the production of hybrid seeds in watermelon. Although fruit development has been studied extensively in watermelon, there are no reports on gene expression in flor...

    Authors: Sun-Ju Rhee, Minseok Seo, Yoon-Jeong Jang, Seoae Cho and Gung Pyo Lee
    Citation: BMC Genomics 2015 16:914
    Content type: Research article Published on:

  27. The development of powerful new methods for DNA sequencing enable the discovery of sequence variants, their utilization for the mapping of mutant loci, and the identification of causal variants in a single ste...

    Authors: Jabier Gallego-Llamas, Andrew E. Timms, Krista A. Geister, Anna Lindsay and David R. Beier
    Citation: BMC Genomics 2015 16:913
    Content type: Methodology article Published on:

  28. Early aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass ...

    Authors: Charles I. Rinerson, Erin D. Scully, Nathan A. Palmer, Teresa Donze-Reiner, Roel C. Rabara, Prateek Tripathi, Qingxi J Shen, Scott E. Sattler, Jai S. Rohila, Gautam Sarath and Paul J. Rushton
    Citation: BMC Genomics 2015 16:912
    Content type: Research article Published on:

  29. DNA methylation is an important epigenetic mark that can potentially link early life exposures to adverse health outcomes later in life. Host factors like sex and age strongly influence biological variation of...

    Authors: Paul Yousefi, Karen Huen, Veronica Davé, Lisa Barcellos, Brenda Eskenazi and Nina Holland
    Citation: BMC Genomics 2015 16:911
    Content type: Research article Published on:

  30. We describe the pioneering experience of a Spanish family pursuing the goal of understanding their own personal genetic data to the fullest possible extent using Direct to Consumer (DTC) tests. With full infor...

    Authors: Manuel Corpas, Willy Valdivia-Granda, Nazareth Torres, Bastian Greshake, Alain Coletta, Alexej Knaus, Andrew P. Harrison, Mike Cariaso, Federico Moran, Fiona Nielsen, Daniel Swan, David Y. Weiss Solís, Peter Krawitz, Frank Schacherer, Peter Schols, Huangming Yang…
    Citation: BMC Genomics 2015 16:910
    Content type: Research article Published on:

  31. Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In t...

    Authors: Rafael A. Cañas, Isabel Feito, José Francisco Fuente-Maqueda, Concepción Ávila, Juan Majada and Francisco M. Cánovas
    Citation: BMC Genomics 2015 16:909
    Content type: Research article Published on:

  32. Quality control (QC) analysis is an important component in maize breeding and seed systems. Genotyping by next-generation sequencing (GBS) is an emerging method of SNP genotyping, which is being increasingly a...

    Authors: Berhanu Tadesse Ertiro, Veronica Ogugo, Mosisa Worku, Biswanath Das, Michael Olsen, Maryke Labuschagne and Kassa Semagn
    Citation: BMC Genomics 2015 16:908
    Content type: Research article Published on:

  33. Down syndrome (DS) or trisomy 21 is the result of a genetic dosage imbalance that translates in a broad clinical spectrum. A major challenge in the study of DS is the identification of functional genetic eleme...

    Authors: Xavier Bofill-De Ros, Mónica Santos, Maria Vila-Casadesús, Eneko Villanueva, Nuria Andreu, Mara Dierssen and Cristina Fillat
    Citation: BMC Genomics 2015 16:907
    Content type: Research article Published on:

  34. Embryo implantation is a complex, synchronized process that requires establishment of a reciprocal dialogue between a receptive endometrium and developing blastocysts. Recently, microRNAs (miRNAs), known to mo...

    Authors: Kamil Krawczynski, Stefan Bauersachs, Zaneta P. Reliszko, Alexander Graf and Monika M. Kaczmarek
    Citation: BMC Genomics 2015 16:906
    Content type: Research article Published on:

  35. Adult neurogenesis and the incorporation of adult-born neurons into functional circuits requires precise spatiotemporal coordination across molecular networks regulating a wide array of processes, including ce...

    Authors: Tracy A. Larson, Karin L. Lent, Theo K. Bammler, James W. MacDonald, William E. Wood, Melissa L. Caras, Nivretta M. Thatra, Agata Budzillo, David J. Perkel and Eliot A. Brenowitz
    Citation: BMC Genomics 2015 16:905
    Content type: Research article Published on:

  36. We investigated parent-of-origin and allele-specific expression effects on obesity and hepatic gene expression in reciprocal crosses between the Berlin Fat Mouse Inbred line (BFMI) and C57Bl/6NCrl (B6N).

    Authors: Stefan Kärst, Danny Arends, Sebastian Heise, Jan Trost, Marie-Laure Yaspo, Vyacheslav Amstislavskiy, Thomas Risch, Hans Lehrach and Gudrun A. Brockmann
    Citation: BMC Genomics 2015 16:904
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2015 16:1018

  37. Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise ...

    Authors: Steven Witte, Allan Bradley, Anton J. Enright and Stefan A. Muljo
    Citation: BMC Genomics 2015 16:903
    Content type: Research article Published on:

  38. Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this spe...

    Authors: Tifeng Shan, Shaojun Pang, Jing Li, Xia Li and Li Su
    Citation: BMC Genomics 2015 16:902
    Content type: Research article Published on:

  39. Auxin and auxin signaling are involved in a series of developmental processes in plants. Auxin Response Factors (ARFs) is reported to modulate the expression of target genes by binding to auxin response elemen...

    Authors: Kaidong Liu, Changchun Yuan, Haili Li, Wanhuang Lin, Yanjun Yang, Chenjia Shen and Xiaolin Zheng
    Citation: BMC Genomics 2015 16:901
    Content type: Research article Published on:

  41. Mammalian aging is a highly complex process, a full mechanistic understanding of which is still lacking. One way to help understand the molecular changes underlying aging is through a comprehensive analysis of...

    Authors: Ryan R. White, Brandon Milholland, Sheila L. MacRae, Mingyan Lin, Deyou Zheng and Jan Vijg
    Citation: BMC Genomics 2015 16:899
    Content type: Research article Published on:

  42. Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiolog...

    Authors: Xianjun Peng, Linhong Teng, Xueqing Yan, Meiling Zhao and Shihua Shen
    Citation: BMC Genomics 2015 16:898
    Content type: Research article Published on:

  43. Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencep...

    Authors: Rui Wang, Liping Li, Yan Huang, Fuguang Luo, Wanwen Liang, Xi Gan, Ting Huang, Aiying Lei, Ming Chen and Lianfu Chen
    Citation: BMC Genomics 2015 16:897
    Content type: Research article Published on:

  44. Paulownia witches’ broom (PaWB) is a fatal disease of Paulownia caused by a phytoplasma. In previous studies, we found that plants with PaWB symptoms would revert to a healthy morphology after methyl methane s...

    Authors: Guoqiang Fan, Xibing Cao, Suyan Niu, Minjie Deng, Zhenli Zhao and Yanpeng Dong
    Citation: BMC Genomics 2015 16:896
    Content type: Research article Published on:

  45. FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most ...

    Authors: Joseph E. Kumka and Carl E. Bauer
    Citation: BMC Genomics 2015 16:895
    Content type: Research article Published on:

  46. Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of pheno...

    Authors: Magretha Diane Wang, Kennedy Dzama, Charles A. Hefer and Farai C. Muchadeyi
    Citation: BMC Genomics 2015 16:894
    Content type: Research article Published on:

  47. Chlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics of C. pecorum strains from sheep, cattle and koalas has revealed that only si...

    Authors: Martina Jelocnik, Nathan L. Bachmann, Bernhard Kaltenboeck, Courtney Waugh, Lucy Woolford, K. Natasha Speight, Amber Gillett, Damien P. Higgins, Cheyne Flanagan, Garry S. A. Myers, Peter Timms and Adam Polkinghorne
    Citation: BMC Genomics 2015 16:893
    Content type: Research article Published on:

  48. Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality o...

    Authors: Annalisa Astolfi, Milena Urbini, Valentina Indio, Margherita Nannini, Chiara Giusy Genovese, Donatella Santini, Maristella Saponara, Anna Mandrioli, Giorgio Ercolani, Giovanni Brandi, Guido Biasco and Maria A. Pantaleo
    Citation: BMC Genomics 2015 16:892
    Content type: Research article Published on:

  49. Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contri...

    Authors: Diego Forni, Diana Martin, Razan Abujaber, Andrew J. Sharp, Manuela Sironi and Edward J. Hollox
    Citation: BMC Genomics 2015 16:891
    Content type: Research article Published on:

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BMC Genomics

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